Note that if you manually change the TV input then the harmony loses track of where it is in the list so the next time you select an activity it may be off.

What hhatkin is saying is there may be a discrete input selection command so that you don't have to use the cycle method - that is definitely preferred. But if you must use the cycle method:

First check the list of inputs on the TV against the list in the harmony setup and make sure they match exactly - number and position. If they do and it still comes up one short then it's probably missing an input command - try increasing the inter-device delay for the TV. Make it a very large number (5000 ms e.g.) for testing and if that works reliably then go back to the original value and increase it a little at a time until it works reliably.